Merge pull request #6572 from RosettaCommons/roccomoretti/resize_ligand_puzzles
[Foldit] Some initial baseline reworking to help support multiple ligands/resizing.
The list of ligand designable positions in the SessionConfig is a mal-feature. If the pose changes size (e.g. if there's insertions or deletions, or if we fragment the designable ligands), then this numbering can become wrong. The proper place for this information is the ReferenceInfo, which gets properly resized when the structure is resized. We already have this info present, so make sure we use it.
This also cleans up a bunch of direct usage of the ReferenceInfo variables, in favor of the get_ligand_designable_positions() utility function.
(No release notes: internal cleanup only.)